VoltRon

Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration

Website | Tutorials | Preprint

VoltRon is a spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is also capable of analyzing multiple types of spatially-aware data modalities.

Staying up-to-date

To ask questions please use VoltRon discussion forum on google groups.

• https://groups.google.com/forum/#!forum/voltron_discussion

Installation

Install from the GitHub repository using devtools (with R version 4.3.0 or higher):

if (!require("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("BIMSBbioinfo/VoltRon")

Depending on the number of required dependencies, installation may be completed under a minute or may take a few minutes.

On Windows and MacOS, OpenCV will be downloaded automatically upon installation. However, Rtools may be required to be downloaded too, hence this may take some time!

On Ubuntu we provide a set of instructions that may help users to build OpenCV with necessary headers here.

On Fedora you may need opencv-devel:

yum install opencv-devel

Dependencies

VoltRon incorporates RBioformats package to import images from ome.tiff files, which requires Java JDK to be available in your system:

See https://cran.r-project.org/web/packages/rJava below for more information.

Docker Hub

You can also run VoltRon from a container already available in Docker Hub. The docker image is based on the Rocker Project and can be run from the terminal like below:

docker run --rm -ti -e PASSWORD=<yourpassword> -p 8787:8787 amanukyan1385/rstudio-voltron:main

Then, start the RStudio session from the browser at http://localhost:8787/ and enter rstudio as username and <yourpassword> as password.

See here for more instructions on how to run the container using Docker Desktop.

References

Manukyan, A., Bahry, E., Wyler, E., Becher, E., Pascual-Reguant, A., Plumbom, I., ... & Akalin, A. (2023). VoltRon: A Spatial Omics Analysis Platform for Multi-Resolution and Multi-omics Integration using Image Registration. bioRxiv, 2023-12.